There are provided a control circuit of a DC-DC converter of a synchronous rectification system which can realize rapid lowering of an output voltage with low power consumption at the stop of power supply, and a control method thereof. While a power supply stop signal is at low level, a control part controls an NMOS transistor according to the output signals of a comparator and a flip-flop circuit. While the power supply stop signal is at high level, the control part masks a reverse current detection signal and the output signal of the flip-flop circuit to control the NMOS transistor according to a detection signal of a comparator. When a choke coil current is reversely flowed and an output voltage is lowered to an output reference voltage corresponding to a reference voltage, the NMOS transistor is brought to the non-conductive state to regenerate the electric power to an input terminal.